rs762950368
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4BP6BS2
The NM_001271.4(CHD2):āc.4165A>Cā(p.Lys1389Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000693 in 1,586,574 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K1389E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001271.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.4165A>C | p.Lys1389Gln | missense_variant | 33/39 | ENST00000394196.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.4165A>C | p.Lys1389Gln | missense_variant | 33/39 | 5 | NM_001271.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000199 AC: 3AN: 151098Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000557 AC: 8AN: 1435476Hom.: 0 Cov.: 30 AF XY: 0.00000840 AC XY: 6AN XY: 713886
GnomAD4 genome AF: 0.0000199 AC: 3AN: 151098Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73762
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2019 | The p.K1389Q variant (also known as c.4165A>C), located in coding exon 32 of the CHD2 gene, results from an A to C substitution at nucleotide position 4165. The lysine at codon 1389 is replaced by glutamine, an amino acid with some similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Developmental and epileptic encephalopathy 94 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at